Output
fort.44 - calculated solvent
accessibilities for each accessible atom of solutes 1 and 2
fort.55 - complexes satisfying
2-contact reaction conditions defined by
iwrec and nwrec, or a complete trajectory
whose
number is given by
nrec. These
complexes can be processed further to make a movie of a Brownian
dynamics
trajectory, to visualize encounter complexes or check interaction
energies calculated by SDA, using
auxiliary
programs from SDA distribution.
fort.66 - a table giving the
length (number of BD steps) of each trajectory. >
fort.77 - this file contains
the values of
the electrostatic and desolvation potentials of solute 1 and solute 2
along 5 selected lines in
3-dimensional
space; a section through the exclusion grid in ascii format in the
plane
passing through the center of the solute 1; reaction atom
information. This file is designed to assist in checking if the
input files are
correct and/or read as expected.
fort.99 - this file gives the
occurrence of
reaction atom
contacts.
The first half of this file gives the number of contacts observed at
each
specified
contact distance for each pair of reaction atoms. In the second
half, the number of contacts is counted differently - only the
first occurrence of the contact in a Brownian dynamics
run/trajectory is counted.
The file with the name specified in BLOCK 13 of the input file has
intermediate results
written every
nprint runs. It can
be
used to check the status of a long SDA run, or to compute association
rate constants from incomplete runs of SDA. It has a table of
fractions of reactive trajectories among the trajectories so far
simulated.
fort.6 - standard output
contains a description of the Brownian dynamics run course and
results.
- Parameters of simulations as read in from input file(s).
- Each nprint runs, the number of
runs
done and the ratio of reaction events at every reaction distance are
printed.
This allows the main results (association rate constants) to be
retrieved in
the case that the program is interrupted before it finishes.
- Mean residence times are computed and printed (after the
simulations are finished) every 1
Å
slab of inter-solute center-to-center separation.
- The main results of simulations - the association rate constants
- are
printed
for every distance window and every number of contact pairs.
- The execution time of the program is printed for
initialization
and simulation parts.
- At the end of the simulations, the statistics over all
runs are
computed and printed out. These are:
- number of Brownian dynamics steps during all simulations;
- the duration of simulations in ps;
- above value scaled per run;
- number of solute overlaps (when the step is repeated) that
occurred;
- number of boosts, when the solutes were artificially
displaced.